What is the difference between is_a and instanceof?

Actually, is_a is a function, whereas instanceof is a language construct. is_a will be significantly slower (since it has all the overhead of executing a function call), but the overall execution time is minimal in either method.

It's no longer deprecated as of 5.3, so there's no worry there.

There is one difference however. is_a being a function takes an object as parameter 1, and a string (variable, constant, or literal) as parameter 2. So:

is_a($object, $string); // <- Only way to call it

instanceof takes an object as parameter 1, and can take a class name (variable), object instance (variable), or class identifier (class name written without quotes) as parameter 2.